Wind, 2-3x lifesize images with MPR-65 and hand-held results in a series of images jumping all over the screen.

Given that description, my recommendation is to forget stacks and use your best single frames.

If you do feel compelled to stack, then I suggest trying Photoshop. I would not be surprised if Photoshop's built-in focus stacking produces a less bad result than either Zerene Stacker or Helicon Focus, given this sort of flawed input.

As for getting a clean result from a stack with that description, I strongly doubt that you'll be able to achieve that goal. Motion of the wind would not only have moved the subject sideways in the frame, but also moved it forwards and backwards, and probably twisted it. The real killer will be the twists, which cause the subject to apparently change shape. Even if you rearrange the images into depth order, any twists will prevent the subject from lining up properly from one frame to another.

The reason I recommend Photoshop in this case is that it's better than the other tools at not producing obvious artifacts when given source material that cannot be aligned correctly.

As for your specific question about preferences, your best shot is to make the percentage values large. Making them too small will guarantee that proper alignment cannot be achieved. With large values, there's at least some chance that the alignment will work out OK, even though that's still not the way to bet.